The towering forward latched on to a terrible defensive header from Ben Coker to nod the ball into the back of the net from close range.
That was enough to condemn the Shrimpers to a fourth successive defeat and a second on the spin at Roots Hall.
Despite the scoreline, Southend started brightly with Freddy Eastwood and Ryan Leonard both firing over from long range before the latter headed a right-wing cross from Kevan Hurst straight at Scunthorpe goalkeeper Sam Slocombe.
Michael Timlin then fired inches wide from 20 yards and, after the break, Hurst went close from a similar distance.
But Iwelumo's goal, which came in the 64th minute, saw the Iron take control and they could have netted more in the closing stages.
Terry Hawkridge saw a deflected 20-yard shot fly inches wide of the left post before Sean McAllister's long-range effort was impressively saved by Southend 'keeper Daniel Bentley.